set head parameters for vb_job_head_3shell
head_parm = vb_set_head_parm;
--- Setting for Output file [relative path from 'proj_root']
head_parm.head_file : Base name for head model
--- Setting for Output surface
head_parm.Nsurf : Number of shell (=1 for MEG , =3 for EEG [default])
head_parm.Nvertex : number of vertex in each surface
= [2000] (Default)
--- Setting for MRI input file (Absolute path)
head_parm.analyze_file : MRI image file
--- Setting for Scalp input file (Absolute path) [There are 2 cases]
If the following files are specified at the same time,
priority order is fs_scalp_file > face_file
1. head_parm.face_file : face file made by vbmeg
2. head_parm.fs_scalp_file : FreeSurfer Scalp ('outer_skin_surface.asc')
--- Setting for CSF input files (Absolute path) [There are 3 cases]
We recommend to use both FreeSurfer and Segment files:
'freesurf_file' + 'gray_file' + 'brain_file'
1. FreeSurfer file Case
head_parm.freesurf_file : FreeSurfer CSF ('inner_skull_surface.asc')
2. Segment file Case
head_parm.brain_file : Brain model file (.brain.mat)
head_parm.gray_file : Gray matter segment file made by SPM 'Segment'
3. Curry file Case
head_parm.curry_file : Curry surface file
%% --- Advanced Optional Parameter
parm.Scalp_mode
= 0 : Scalp surface is intersection of face and dilated CSF [Default]
= 1 : Scalp surface is smoothed face & Skull is the same as mode=0
= 2 : Scalp surface is smoothed face & Skull is erosion of face
--- Optional setting for outer Skull surface (Absolute path)
parm.fs_skull_file : Outer Skull surface ('/outer_skull_surface.asc')
--- Radius of Morphology operation [mm]
If the obtained shell model is not good,
you can adjust the following morphology radius parameters
parm.Radius_scalp = 4 : Thickness of Scalp [mm]
parm.Radius_skull = 2 : Min Thickness of Skull [mm]
parm.Radius_fs : smoothing radius for FreeSurfer surface
= [4 -4 ] Default (No size change)
parm.Radius_csf : smoothing radius for Gray matter
= [6 6 -7 ] Default (Expand 6 mm)
parm.Radius : smoothing radius for CSF surface
= [4 -4 ] Default (No size change)
parm.Nloop = 200; Iteration number for fit boundary
parm.Nlast_csf = 10 ; Iteration number for CSF smoothing by spring model
As Nlast becomes larger, surface becomes smoother
but it shrinks inward
parm.Nlast_scalp = 0 ; Iteration number for Scalp
parm.Nlast_skull = 0 ; Iteration number for Skull
(Gray matter parameters)
parm.Glevel = [0.8]; level of gray matter selection threshold
parm.Radius_gray = [-2 2]; Radius to remove noise in gray matter image
(Brain model parameters)
parm.Radius_fill = [6]; Cortex fill radius
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function head_parm = vb_set_head_parm 0002 % set head parameters for vb_job_head_3shell 0003 % head_parm = vb_set_head_parm; 0004 % --- Setting for Output file [relative path from 'proj_root'] 0005 % head_parm.head_file : Base name for head model 0006 % --- Setting for Output surface 0007 % head_parm.Nsurf : Number of shell (=1 for MEG , =3 for EEG [default]) 0008 % head_parm.Nvertex : number of vertex in each surface 0009 % = [2000] (Default) 0010 % 0011 % --- Setting for MRI input file (Absolute path) 0012 % head_parm.analyze_file : MRI image file 0013 % 0014 % --- Setting for Scalp input file (Absolute path) [There are 2 cases] 0015 % If the following files are specified at the same time, 0016 % priority order is fs_scalp_file > face_file 0017 % 1. head_parm.face_file : face file made by vbmeg 0018 % 2. head_parm.fs_scalp_file : FreeSurfer Scalp ('outer_skin_surface.asc') 0019 % 0020 % --- Setting for CSF input files (Absolute path) [There are 3 cases] 0021 % We recommend to use both FreeSurfer and Segment files: 0022 % 'freesurf_file' + 'gray_file' + 'brain_file' 0023 % 0024 % 1. FreeSurfer file Case 0025 % head_parm.freesurf_file : FreeSurfer CSF ('inner_skull_surface.asc') 0026 % 2. Segment file Case 0027 % head_parm.brain_file : Brain model file (.brain.mat) 0028 % head_parm.gray_file : Gray matter segment file made by SPM 'Segment' 0029 % 0030 % 3. Curry file Case 0031 % head_parm.curry_file : Curry surface file 0032 % 0033 %%% --- Advanced Optional Parameter 0034 % parm.Scalp_mode 0035 % = 0 : Scalp surface is intersection of face and dilated CSF [Default] 0036 % = 1 : Scalp surface is smoothed face & Skull is the same as mode=0 0037 % = 2 : Scalp surface is smoothed face & Skull is erosion of face 0038 % 0039 % --- Optional setting for outer Skull surface (Absolute path) 0040 % parm.fs_skull_file : Outer Skull surface ('/outer_skull_surface.asc') 0041 % 0042 % --- Radius of Morphology operation [mm] 0043 % If the obtained shell model is not good, 0044 % you can adjust the following morphology radius parameters 0045 % 0046 % parm.Radius_scalp = 4 : Thickness of Scalp [mm] 0047 % parm.Radius_skull = 2 : Min Thickness of Skull [mm] 0048 % parm.Radius_fs : smoothing radius for FreeSurfer surface 0049 % = [4 -4 ] Default (No size change) 0050 % parm.Radius_csf : smoothing radius for Gray matter 0051 % = [6 6 -7 ] Default (Expand 6 mm) 0052 % parm.Radius : smoothing radius for CSF surface 0053 % = [4 -4 ] Default (No size change) 0054 % 0055 % parm.Nloop = 200; Iteration number for fit boundary 0056 % parm.Nlast_csf = 10 ; Iteration number for CSF smoothing by spring model 0057 % As Nlast becomes larger, surface becomes smoother 0058 % but it shrinks inward 0059 % parm.Nlast_scalp = 0 ; Iteration number for Scalp 0060 % parm.Nlast_skull = 0 ; Iteration number for Skull 0061 % (Gray matter parameters) 0062 % parm.Glevel = [0.8]; level of gray matter selection threshold 0063 % parm.Radius_gray = [-2 2]; Radius to remove noise in gray matter image 0064 % (Brain model parameters) 0065 % parm.Radius_fill = [6]; Cortex fill radius 0066 % 0067 % Copyright (C) 2011, ATR All Rights Reserved. 0068 % License : New BSD License(see VBMEG_LICENSE.txt) 0069 0070 % --- Setting for Output file 0071 % [relative path from 'proj_root'] 0072 head_parm.head_file = []; 0073 0074 % --- Setting for MRI input file 0075 % (Absolute path) 0076 head_parm.analyze_file = 'Subject.nii'; 0077 0078 % --- Setting for Scalp input file [There are 2 cases] 0079 % 1. head_parm.face_file : face file made by vbmeg 0080 % 2. head_parm.fs_scalp_file : FreeSurfer Scalp ('outer_skin_surface.asc') 0081 0082 % (Absolute path) 0083 % head_parm.face_file = []; 0084 head_parm.fs_scalp_file = 'bem/outer_skin_surface.asc'; 0085 0086 % --- Setting for CSF input files [There are 3 cases] 0087 % 1. FreeSurfer file Case 0088 % 2. Segment file Case 0089 % 3. Curry file Case 0090 % We recommend to use 'freesurf_file' + 'gray_file' + 'brain_file' 0091 0092 % Relative path from 'proj_root' 0093 head_parm.brain_file = 'Subject.brain.mat'; 0094 0095 % (Absolute path) 0096 head_parm.freesurf_file = 'bem/inner_skull_surface.asc'; 0097 head_parm.gray_file = 'c1Subject.nii'; 0098 % head_parm.curry_file = []; 0099 0100 0101 % Number of surface 0102 % Default is 3 shell model 0103 head_parm.Nsurf = 3; 0104 head_parm.Nvertex = [2000]; 0105 0106 %%% --- Advanced Optional Parameters 0107 %%% Usually, there is no need to change the following parameters 0108 %%% In the case where the result is not good, you can try again 0109 %%% by changing the following parameters 0110 0111 % Set Default Radius parameters 0112 head_parm.Radius_fs = [4 -4]; 0113 head_parm.Radius_csf = [6 6 -7 ] ; 0114 head_parm.Radius_scalp = 4; 0115 head_parm.Radius_skull = 2; 0116 head_parm.Skull_ratio = 0.5; 0117 0118 head_parm.Radius = [4 -4 ] ; 0119 head_parm.Radius_final = [4 -4]; 0120 0121 head_parm.Radius_fill = [6]; 0122 head_parm.Radius_gray = [-2 2]; 0123 head_parm.Glevel = [0.8]; 0124 0125 head_parm.Nloop = 200; 0126 0127 head_parm.Nlast_csf = 10 ; 0128 head_parm.Nlast_scalp = 0 ; 0129 head_parm.Nlast_skull = 0 ; 0130 0131 0132 % Scalp_mode 0133 head_parm.Scalp_mode = 0; 0134 0135 % subsampling size for mask image [mm] 0136 if vb_matlab_version > 6, 0137 head_parm.vstep = 1; 0138 else 0139 head_parm.vstep = 2; 0140 end 0141